Contacts of the strand formed by residues 3624 - 3629 (chain A) in PDB entry 2RT5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR3624 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3533A LEU* 3.9 23.6 - - + +
3536A ARG* 3.0 42.5 + - + -
3537A SER* 4.5 12.3 - - - -
3612A ILE 3.2 1.4 - - - +
3613A ASN* 3.0 29.3 + - - -
3614A VAL* 3.3 33.5 + - + +
3616A ASN* 3.7 25.8 - - + -
3621A GLN* 4.1 8.3 - - + -
3622A PRO 2.8 4.6 + - - -
3623A ALA* 1.3 87.0 - - + +
3625A VAL* 1.3 62.7 + - - +
3626A LEU* 4.0 1.6 - - + -
3661A ILE* 4.5 7.6 - - + -
3662A ALA 4.1 10.1 - - - -
3663A SER* 4.0 11.1 + - - -
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Residues in contact with VAL3625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3551A GLN* 5.0 1.1 - - - +
3566A ARG* 5.8 0.2 - - - +
3611A ILE* 3.4 24.9 - - + -
3612A ILE 3.7 2.2 - - - -
3613A ASN* 3.4 21.1 - - - +
3623A ALA 5.5 2.0 - - - +
3624A TYR* 1.3 74.1 - - - +
3626A LEU* 1.3 61.3 + - - +
3627A GLN* 3.4 30.1 - - + +
3660A VAL 3.0 3.1 - - - +
3661A ILE* 3.4 0.7 - - - -
3662A ALA* 2.7 48.4 + - + +
3664A VAL 4.8 11.2 - - - +
2518B TYR* 4.7 17.7 - - + +
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Residues in contact with LEU3626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3537A SER* 4.0 8.5 - - - +
3538A LEU* 3.4 32.8 - - + -
3547A LEU* 4.0 15.3 - - + -
3610A GLY 2.7 23.6 - - - +
3611A ILE* 3.3 1.4 - - - -
3612A ILE* 2.8 47.8 + - + +
3614A VAL* 3.6 31.6 - - + -
3624A TYR 4.5 1.1 - - - +
3625A VAL* 1.3 76.3 - - - +
3627A GLN* 1.3 54.2 + - - +
3628A ILE* 4.3 0.4 - - + +
3659A ILE* 3.8 16.6 - - + -
3660A VAL 3.3 3.6 - - - -
3661A ILE* 3.7 25.1 - - + -
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Residues in contact with GLN3627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3553A MET* 3.1 34.1 - - - -
3563A VAL* 4.5 3.4 - - - +
3566A ARG* 3.5 19.8 + - - +
3609A ALA* 3.9 5.4 - - + -
3610A GLY 3.6 2.2 - - - -
3611A ILE* 3.5 9.2 - - + -
3625A VAL* 3.4 23.6 - - + -
3626A LEU* 1.3 70.3 - - - +
3628A ILE* 1.3 62.0 + - - +
3629A PHE* 3.4 25.6 + - + -
3658A MET 3.0 8.3 - - - +
3659A ILE* 3.1 0.7 - - - -
3660A VAL* 2.7 61.6 + - + +
3662A ALA* 3.8 10.7 - - - +
2518B TYR* 3.9 2.5 + - - -
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Residues in contact with ILE3628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3513A LEU* 3.9 21.3 - - + -
3549A ILE* 3.6 17.5 - - + -
3603A LEU* 3.5 14.3 - - + +
3609A ALA* 3.2 4.9 - - - -
3610A GLY* 2.7 45.5 + - - +
3612A ILE* 3.4 32.1 - - + -
3626A LEU 4.3 2.7 - - - +
3627A GLN* 1.3 71.3 - - - +
3629A PHE* 1.3 57.5 + - - +
3657A LEU* 3.5 43.7 - - + -
3658A MET 3.8 2.7 - - - -
3659A ILE* 3.8 17.3 - - + -
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Residues in contact with PHE3629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3553A MET* 4.4 8.1 - - - -
3555A LEU* 4.0 32.8 - - + -
3560A LEU* 4.8 2.7 - - + -
3563A VAL* 4.4 12.8 - - + -
3609A ALA* 3.6 18.8 - - + -
3627A GLN* 3.5 46.0 - - + -
3628A ILE* 1.3 72.7 - - - +
3630A PRO* 1.3 67.4 - - + +
3632A CYS* 5.0 0.2 - - - -
3634A PHE* 4.0 19.1 - + + -
3635A SER* 3.9 15.5 - - - +
3657A LEU* 3.5 6.1 - - - +
3658A MET* 2.8 54.6 + - + +
3660A VAL* 3.7 15.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il